392023 Formal methods in Algorithmic Cheminformatics and Systems Biology (V) (WiSe 2024/2025)

The course provides an overview of mathematical and computational modelling and analysis methods commonly employed in the studies of complex systems, with special focus on biological and chemical applications.
By the end of the course, the students should be able to independently judge which modelling and analysis techniques are suitable for a given problem definition.

The following topics are covered in the course:
Different model types and their advantages (deterministic vs non-deterministic models, discrete vs continuous models, qualitative vs quantitative models, generative vs agent-based models), Petri nets, Boolean networks, Markov chains and stochastic Petri nets, Kappa (site graph transformation), stochastic simulation, model checking, Petri net unfolding (causal analysis/concurrency), abstract interpretation;

Teilnahmevoraussetzungen, notwendige Vorkenntnisse

No strict requirements, but at least foundational knowledge of formal methods in software verification, or of graph theory and algorithms, mathematical logic, formal languages, grammars and automata is encouraged.